Yeah i gotta agree, she probably signed her mother's death warrant with that comment, if not now then later once elincia gets her own people.
On another note, this might be my favorite take on "emperor dad of switched at bith daughters" that i've read so far. He admits what he's done was neglect and doesn't try and shift the blame or pretend it never happened. Also he recognizes that philomel isnt his biological daughter but says he loved her as his own, and still does. A lot of manga/manhwa/CN's treat blood relation as paramount, where the missing daughter comes back and there's an instant connection with the family members, or the "fake" daughter either never bonded with family members (thats usually explained by having an 'outsiders' blood), or worse, the previously loved daughter is kicked out the door, as if those 15-20 years of affection meant nothing. Here the emperor states his love for the fake daughter as real and undiminished (which at least appears to be true), and treats the previously unknown biological daughter almost as a stranger (which she is). Even the way he worded it, "...if you hadn't brought her back i never would have known about her.." speaks more towards responsibility than some fantastical longing for his flesh and blood child. That could just be the translation team giving it added nuance (thank you for all your hard work, by the way) but this Emperor/Father character seems much more levelheaded and rational than many others i've seen.